Step 2.4: Import gff from prepared file

This step imports the data from the prepared .gff file (Step 2.3) into the specified core database.

cd ~/import
perl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini

If more than one .gff was prepared during Step 2.3 (due to exceptions that required different pattern matching), each of the .ini files can be passed to this step in a single command to load all gene models at once.

perl ../ei/core/import_gene_models.pl ../ei/conf/core-import.ini /path/to/exception.ini

Configuration options

• [DATABASE_CORE]

[DATABASE_CORE]
	NAME = operophtera_brumata_v1_core_31_84_1
	HOST = localhost
	PORT = 3306
	RW_USER = importer
	RW_PASS = importpassword
	RO_USER = anonymous
	RO_PASS =

This must refer to the same database as used in Step 2.2: Create database and load sequence data.

• [MODIFY]

[MODIFY]
	TRUNCATE_GENE_TABLES = 1

If TRUNCATE_GENE_TABLES is set, all tables that are associated with specific gene models will be truncated allowing for a fresh import of the data. Otherwise, only additional data will be imported.